Diagnosis
This is common. The frame template is generic, and wood tops can have slight variance. You need to shift the frame or drill new pilot holes.
How to Fix It
Loosely place the frame on the underside of the tabletop. Align it where you want it. Use a pencil to mark through 2-3 of the pre-drilled holes that DO align. Drill small pilot holes (1/8" bit) at your new marks. Secure the frame with the provided bolts at these points. The other holes can be left unused.
If That Didn't Work
If no holes align, you must create all new mounting points. Measure carefully to ensure the frame is centered and square before marking and drilling all pilot holes.
Heads Up
Do not force the bolts. If they won't thread in, you are not aligned. Forcing them will strip the particleboard, creating a weak mount. Always use pilot holes.